It has been supported on DS14 shelves, I cannot see why it would not be supported on the DS4243. However, you would not want to mix drive types or speeds.
As to whether you should have a second aggregate, keep in mind if you use 2TB drives in an aggr of 1TB drives, all of the 2TB drives will be right sized down to 1TB, thus wasting 12TB of space(1 x 12). Running ONTAP 8.0.1 allows you put all 12 x 2TB drives into one aggregate, thus you could only lose 6TB, 2 x parity and 1 x spare.
However, this won't be very high spec'd for performance because only 9 spindles will actually be used for data. If this is a secondary/backup build like our 2TB drive based systems, the performance should not be a concern.
- Scott
